The cloud forests of Mesoamerica are highly endangered habitats and the existence of narrowly distributed cryptic endemics will increase the number of taxa at potential risk of extinction. Here, we investigate genetic divergence between populations of the azure-crowned hummingbird (Amazilia cyanocephala), a species complex of endemic hummingbirds to the montane forests of Mesoamerica, by analysing DNA sequences of four mitochondrial markers, morphological data and ecological niche modelling. Our results revealed the presence of two mtDNA lineages corresponding to subspecies A. c. cyanocephala distributed from Tamaulipas to Chiapas in Mexico and Amazilia c. guatemalensis distributed from southern Chiapas to Guatemala. The lineage split can be explained as a consequence of relative isolation of the populations in the different mountain ranges separated by the Motagua-Polochic-Jocotán fault system and corresponds to differences in morphology and to the lack of overlap in environmental space between subspecies. The divergence time estimates do not support the proposed model of a highly constrained temporal window at the end of the Pliocene as divergence at this barrier between cyanocephala and guatemalensis and splits of other bird taxa occurred during the Pleistocene.